Efforts are underway to map genes and regulatory elements throughout the human genome. ENCODE-Consortium et al., Science 306:636-640 (2004). The goals of these efforts are to identify many different types of elements, including those involved in gene regulation, DNA replication and genome organization in general. However, currently thorough identification of genes and regulatory elements has only been performed for a selected 1% of the human genome.
In order to fully annotate the human genome and to understand its regulation, a complete gene map of all functional elements should also determine and define the relationships between them. For instance, for each gene it needs to be established by which elements it is regulated. This is complicated by the fact that the genomic positions of genes and elements do not provide direct information about functional relationships between them. A well-known example is provided by enhancers that can regulate multiple target genes that are located at large genomic distances or even on different chromosomes without affecting genes immediately next to them (Spilianakis et al., Nature 435: 637-645 (2005); and West et al., Hum Mol Genet. 14:R101-111 (2005)).
What is needed in the art is a high-throughput method that can isolate interactions between genes and gene regulatory elements as well as interactions between regulatory elements themselves combined with methods to quantify the occurrence of such interactions.